Abstract: A method is presented for reprogramming cells of a subject. As a starting point, a biological sample of a sample cell is received from the subject, where the sample cell has a given cell type. The method includes: determining gene expression data for the sample cell from the biological sample; receiving gene expression data for a target cell having a target cell type, where the target cell type differs from the given cell type; deriving a state transition matrix which models cell dynamics; computing a regulatory set for a given transcription factor, where the regulatory set quantifies influence of the given transcription factor on a genome; expressing reprogramming of the sample cell to the target cell with a state-space representation of a linear system; and solving for the input vector in the state-space representation.